1C7K

CRYSTAL STRUCTURE OF THE ZINC PROTEASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • R-Value Free: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of the zinc-binding site in the crystal structure of a zinc endoprotease from Streptomyces caespitosus at 1 A resolution.

Kurisu, G.Kai, Y.Harada, S.

(2000) J.Inorg.Biochem. 82: 225-228


  • PubMed Abstract: 
  • A zinc endoprotease produced by Streptomyces caespitosus (ScNP) contains a H83E84TGH87VLG90LPD93-Met103 sequence. Except for D93, this amino acid sequence is the same as a characteristic consensus HEXXHXXGXXH-M motif found in one class of zinc endopr ...

    A zinc endoprotease produced by Streptomyces caespitosus (ScNP) contains a H83E84TGH87VLG90LPD93-Met103 sequence. Except for D93, this amino acid sequence is the same as a characteristic consensus HEXXHXXGXXH-M motif found in one class of zinc endoprotease called 'metzincins'. We analyzed the structural and functional role of the consensus sequence located around a catalytically essential zinc ion based on the crystal structure of ScNP. The structure was determined at the highest level on resolution (1 A resolution) and accuracy among crystal structures of zinc endoproteases ever determined. The zinc ion of ScNP is tetrahedrally coordinated by three amino acid side-chains (H83, H87 and D93) and a water molecule. The distances between the zinc ion and the coordinating atoms are 2.01, 2.01 and 1.95 A for H83N epsilon, H87N epsilon and D93O delta, respectively. These distances agree very well with those normally found in crystal structures of zinc-containing small molecules in the Cambridge Structural Database. On the other hand, the distance between the zinc ion and the coordinating water molecule (1.93 A) is slightly shorter than the typical value (2.01 A) found in the database. In addition, E84O epsilon makes a short hydrogen bond to this water molecule with the distance of 2.54 A. Two hydrogen bonds (H83N delta-L102O, H87N delta-L91O) and van der Waals interactions between the side-chain of M103 and the two imidazole rings of H83 and H87 are also observed. These interactions are probably important for the imidazole rings to construct the tetrahedral coordination arrangement toward the zinc ion.


    Related Citations: 
    • Crystallization and Main-Chain Structure of Neutral Protease from Streptomyces caespitosus
      Harada, S.,Kitadokoro, K.,Kinoshita, T.,Kai, Y.,Kasai, N.
      (1991) J.BIOCHEM.(TOKYO) 110: 46
    • Complete Amino Acid Sequence of a Zinc Metalloendoprotease from Streptomyces caespitosus
      Harada, S.,Kinoshita, T.,Kasai, N.,Tsunasawa, S.,Sakiyama, F.
      (1995) Eur.J.Biochem. 233: 683
    • Structure of the Zinc Endoprotease from Streptomyces caespitosus
      Kurisu, G.,Kinoshita, T.,Sugimoto, A.,Nagara, A.,Kai, Y.,Kasai, N.,Harada, S.
      (1997) J.BIOCHEM.(TOKYO) 121: 304


    Organizational Affiliation

    Department of Materials Chemistry, Graduate School of Engineering, Osaka University, Suita, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ZINC ENDOPROTEASE
A
132Streptomyces caespitosusGene Names: snpA
EC: 3.4.24.77
Find proteins for P56406 (Streptomyces caespitosus)
Go to UniProtKB:  P56406
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • R-Value Free: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.103α = 90.00
b = 55.199β = 90.00
c = 37.243γ = 90.00
Software Package:
Software NamePurpose
SHELXSphasing
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-04-25
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description